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CHE 214: Biochemistry
Lecture Two
TOPICS;
•LIPIDS
•PROTEINS
•NUCLEIC ACIDS

Lecturer: Dr. G. Kattam Maiyoh

February 21, 2013 GKM/CHE 214/LEC 02/SEM 02/2013 1

Lipids
• Lipids include the following;
– Fatty acids (Polymers of CH2 units)
– Glycerol
– Triglycerides
– Other subunits (phosphate, choline, etc) may be
attached to yield “phospholipids”
• Charged phosphate groups will create a polar molecule
with a hydrophobic (nonpolar) end and a hydrophillic
(polar) end


Lipids


Phospholipids


Phospholipid bilayer

Hydrophillic heads

Hydrophobic tails


Steroids


c. Proteins
• Proteins serve many essential roles in the cell
– Polymers of amino acids
– There are 20 naturally occurring amino acids
• A few modified amino acids are also used (rare)
• The large number of amino acids allows huge diversity
in amino acid sequence

N = # of amino acids in a protein
N20 = # of possible combinations


Protein Function
Some examples
• Structure- form structural components of the cell including:
– Cytoskeleton / nuclear matrix / tissue matrix

• Movement - Coordinate internal and external movement of cells,
organelles, tissues, and molecules.
– Muscle contraction, chromosome separation, flagella………
• Micro-tubueles, actin, myosin

• Transport-regulate transport of molecules into and out of the cell /
nucleus / organelles.
• Channels, receptors, dynin, kinesin

• Communication-serve as communication molecules between different
organelles, cells, tissues, organs, organisms.
– Hormones


Protein Function
Some examples
• Chemical Catalyst – serves to make possible all of the
chemical reactions that occur within the cell.
– Enzymes (thousands of different enzymes)

• Defense-recognize self and non-self, able to destroy
foreign entities (bacteria, viruses, tissues).
– Antibodies, cellular immune factors

• Regulatory-regulates cell proliferation, cell growth, gene
expression, and many other aspects of cell and organism
life cycle.
– Checkpoint proteins, cyclins, transcription factors


Protein Structure
• Polymers made from 20
different amino acids
– All amino acids have a
Common “core”
• Amino end (N end)
• Acid end (C end, carboxy
end)
– Linked by peptide bond
– 20 different side chains


Properties of amino acids
• amino acids:
acidic
basic
hydrophobic

• Amino acids all have
The same basic structure

• Chemical properties of the
amino acids yield
properties of the protein!

Properties of amino acids


Protein Structure
• The 3-D shape and properties of the protein
determine its function.
• Shape and properties of protein determined
by interactions between individual amino acid
components.
• Four “levels” of protein structure
– Primary (Io), secondary (IIo), tertiary (IIIo), and
quaternary (IVo) (sometimes).


Levels of Protein Structure
• I0 (primary) structure
– Linear order of amino acids in a protein:

– 1AASXDXSLVEVHXXVFIVPPXILQAVVSIA
– 31 T T R X D D X D S A A A S I P M V P G W V L K Q V X G S Q A
– 61 G S F L A I V M G G G D L E V I L I X L A G Y Q E S S I X A
– 91 S R S L A A S M X T T A I P S D L W G N X A X S N A A F S S
– 121 X E F S S X A G S V P L G F T F X E A G A K E X V I K G Q I
– 151 T X Q A X A F S L A X L X K L I S A M X N A X F P A G D X X
– 181 X X V A D I X D S H G I L X X V N Y T D A X I K M G I I F G
– 211 S G V N A A Y W C D S T X I A D A A D A G X X G G A G X M X
– 241 V C C X Q D S F R K A F P S L P Q I X Y X X T L N X X S P X
– 271 A X K T F E K N S X A K N X G Q S L R D V L M X Y K X X G Q
– 301 X H X X X A X D F X A A N V E N S S Y P A K I Q K L P H F D
– 331 L R X X X D L F X G D Q G I A X K T X M K X V V R R X L F L
– 361 I A A Y A F R L V V C X I X A I C Q K K G Y S S G H I A A X
– 391 G S X R D Y S G F S X N S A T X N X N I Y G W P Q S A X X S
– 421 K P I X I T P A I D G E G A A X X V I X S I A S S Q X X X A
– 451 X X S A X X A

Single letter code for amino acids, also a three letter code.
Refer to your genetic code handout.


Levels of Protein Structure
Primary Structure
• Amino acids combine to form a chain
• Each acid is linked by a peptide bond
• Io structure by itself does not provide a lot of
information.


• 20 (secondary) structure
– Based on local interactions between amino acids
• Common repeating structures found in proteins.
– Two types: alpha-helix and beta-pleated sheet.
• In an alpha-helix the polypeptide main chain makes up
the central structure, and the side chains extend out
and away from the helix.
• The CO group of one amino acid (n) is hydrogen
bonded to the NH group of the amino acid four
residues away (n +4).
• From amino acid sequence - Can predict regions of
secondary structure


Ribbon Diagram

α-helical regions


Beta sheet
• Two types;
– Parallel
– anti-parallel


Beta Sheet ribbon diagram

parallel
antiparallel


Protein Structure
• 30 (tertiary structure)
– Complete 3-D structure
of protein (single
polypeptide)

hexokinase

Chymotrypsin with inhibitor


Protein Structure
• 40 (quaternary) structure
– Not all proteins have 40
structure
– Only if they are made of
multiple polypeptide chains


d. Nucleic Acids
• DNA – deoxyribonucleic acid
– Polymer of deoxyribonucleotide triphosphate (dNTP)
– 4 types of dNTP (ATP, CTP, TTP, GTP)
– All made of a base + sugar + triphosphate

• RNA – ribonucleic acid
– Polymer of ribonucleotide triphosphates (NTP)
– 4 types of NTP (ATP, CTP, UTP, GTP)
– All made of a base + sugar + triphosphate

• So what’s the difference?
– The sugar (ribose vs. deoxyribose) and one base (UTP vs.
TTP)

Function
• Nucleic Acids
– Information Storage
• DNA / mRNA
– Information transfer / Recognition
• rRNA / tRNA / snRNA
– Regulatory
• microRNA ?


DNA
•Information for all proteins stored in DNA
in the form of chromosomes or plasmids.
•Chromosomes (both circular and linear)
consist of two strands of DNA wrapped
together in a left handed helix (imagine
screwing inwards)

•The strands of the helix are held together
by hydrogen bonds between the individual
bases.
•The “outside” of the helix consists of
sugar and phosphate groups, giving the DNA
molecule a negative charge.


Complimentary Base Pairs

A-T Base pairing G-C Base Pairing


DNA Structure
• The DNA helix is “anti-parallel”
– Each strand of the helix
has a 5’ (5 prime) end and
a 3’ (3 prime) end.


DNA Structure
3’ end
5 ‘ end

Strand 2 Strand 1
(Crick strand)
(Watson strand)

5’end
3 ‘ end

DNA Structure
1 atgatgagtg gcacaggaaa cgtttcctcg atgctccaca gctatagcgc caacatacag
61 cacaacgatg gctctccgga cttggattta ctagaatcag aattactgga tattgctctg
121 ctcaactctg ggtcctctct gcaagaccct ggtttattga gtctgaacca agagaaaatg
181 ataacagcag gtactactac accaggtaag gaagatgaag gggagctcag ggatgacatc
241 gcatctttgc aaggattgct tgatcgacac gttcaatttg gcagaaagct acctctgagg
301 acgccatacg cgaatccact ggattttatc aacattaacc cgcagtccct tccattgtct
361 ctagaaatta ttgggttgcc gaaggtttct agggtggaaa ctcagatgaa gctgagtttt
421 cggattagaa acgcacatgc aagaaaaaac ttctttattc atctgccctc tgattgtata

Because of the base pairing rules, if we know one
strand we also know what the other strand is.
Convention is to right from 5’ to 3’ with 5’ on the left.


Chromosomes and Plasmids
• Chromosomes are composed of DNA and
proteins.
– Proteins (histone & histone like proteins) serve
a structural role to compact the chromosome.
– Chromosomes can be circular, or linear.
• Both types contain an antiparallel double helix!
– Genes are regions within a chromosome.
• Like words within a sentence.


RNA
• Almost all single stranded (exception is RNAi).
• In some RNA molecules (tRNA) many of the
bases are modified (e.g. psudouridine).
• Has capacity for enzymatic function
-ribozymes
• One school of thought holds that early
organisms were based on RNA instead of DNA
(RNA world).


RNA
• Several different “types” which
reflect different functions
– mRNA (messenger RNA)
– tRNA (transfer RNA)
– rRNA (ribosomal RNA)
– snRNA (small nuclear RNA)
– RNAi (RNA interference)


RNA function
• mRNA – transfers information from DNA to
ribosome (site where proteins are made)
• tRNA – “decodes” genetic code in mRNA, inserts
correct A.A. in response to genetic code.
• rRNA-structural component of ribosome
• snRNA-involved in processing of mRNA
• RNAi-double stranded RNA, may be component of
antiviral defense mechanism.


RNA

A - hairpin loop
B- internal loop
C- bulge loop
D- multibranched loop
E- stem
F- pseudoknot

Complex secondary structures can form in linear molecule


mRNA
• Produced by RNA polymerase as product of
transcription
– Provides a copy of gene sequence for use in
translation (protein synthesis).
– Transcriptional regulation is major regulatory
point
– Processing of RNA transcripts occurs in eukaryotes
• Splicing, capping, poly A addition
– In prokaryotes coupled transcription and
translation can occur


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